ali2gff(1) [debian man page]

ALI2GFF(1)						      General Commands Manual							ALI2GFF(1)

NAME

       ali2gff - Module to translate a MUMmer output files into gff formatted output.

SYNOPSIS

       ali2gff [-r] [-t <.|0|1|2>] [-x <name>] [-y <name>] [-H] [-f] [-h] <MUMmer_output_file>

OPTIONS

       -h, --help
	      Show summary of options.

       -r     Interchange the order of sequences (sequence 1 on y-axis, sequence 2 on x-axis).

       -t <.|0|1|2>
	      Put label 'frame' in gff output.

       -x <name>
	      Specify the species name for species1 (default: "Seq1").

       -y <name>
	      Specify the species name for species2 (default: "Seq2").

       -i     Ignore full sequence identities.

       -f     Write output to file.

SEE ALSO

       blat2gff(1), gff2aplot(1), parseblast(1), sim2gff(1).

AUTHOR

       ali2gff was written by Steffi Gebauer-Jung.

       This manual page was written by Nelson A. de Oliveira <naoliv@gmail.com>, for the Debian project (but may be used by others).

							  Mon, 21 Mar 2005 21:44:15 -0300						ALI2GFF(1)

SIM2GFF(1)						      General Commands Manual							SIM2GFF(1)

NAME

       sim2gff - Converts SIM file into GFF formatted records

SYNOPSIS

       sim2gff [-frxyHh] sim_file > gff_file

DESCRIPTION

       This manual page documents briefly the sim2gff command.

       sim2gff is a program written in Perl that converts SIM file into GFF formatted records (for use with gff2aplot and gff2javaplot).

OPTIONS

       -h, --help
	      Show summary of options.

       -f     Output is written to a file named <sim_file>.gff.

       -r     Interchange the order of sequences (Seq1 on y-axis, Seq2 on x-axis).

       -x <name>
	      Specify the species name for species1 (default: "Seq1").

       -y <name>
	      Specify the species name for species2 (default: "Seq2").

       -H     Use the fasta file headers for species labels.

EXIT STATUS

       The following perl-like exit status are returned:

       0 Error

       1 Successful completion

SEE ALSO

       ali2gff(1), blat2gff(1), gff2aplot(1), parseblast(1).

AUTHOR

       sim2gff was written by Thomas Wiehe <twiehe@imb-jena.de>.

       This manual page was written by Nelson A. de Oliveira <naoliv@gmail.com>, for the Debian project (but may be used by others).

							  Mon, 21 Mar 2005 21:44:15 -0300						SIM2GFF(1)